Sidebar
Sample summary
Input data: infant stools
- n samples = 341
- n features: 251
- mean read count: 10^{6}, s.d. = 0
Alpha diversity
Column
Seroconversion
Blue = seroconversion+, Orange = seroconversion-.
Seroconverion - N by country
IND IND (neo+) IND (neo-) MLW
0 204 104 99 46
1 78 45 33 10Mean + s.d.
seroconv Observed.mean Observed.sd Observed.country
1 0 127.13 33.27 IND
2 1 114.97 27.83 IND
3 0 125.1 31.38 IND (neo+)
4 1 117.91 26.21 IND (neo+)
5 0 129.42 35.31 IND (neo-)
6 1 110.97 29.84 IND (neo-)
7 0 153.02 25.51 MLW
8 1 127.1 27.77 MLWSeroconverion - P values
[,1]
IND 0.010349
MLW 0.011566
IND_exposed 0.083064
IND_nonexposed 0.000460RV-IgA
Correlation heatmap
Collated results
rho p n
IND -0.0701 0.240417 282
IND (neo+) 0.0184 0.823871 149
IND (neo-) -0.1276 0.144694 132
MLW -0.2226 0.099098 56Dose 1 shedding
Blue = shed+, Orange = shed-.
Dose 1 shedding - N by country
IND IND (neo+) IND (neo-) MLW
0 207 122 83 26
1 74 25 49 21Mean + s.d.
dose1_shedding Observed.mean Observed.sd Observed.country
1 0 125.46 30.77 IND
2 1 119.92 35.86 IND
3 0 124.27 30.47 IND (neo+)
4 1 118.84 27.62 IND (neo+)
5 0 127.37 31.64 IND (neo-)
6 1 120.47 39.66 IND (neo-)
7 0 152.5 27.46 MLW
8 1 143.95 32.17 MLWDose 1 shedding - P values
[,1]
IND 0.149347
MLW 0.319564
IND_exposed 0.159921
IND_nonexposed 0.113114Beta diversity
Column
Seroconversion
Summary
R2 p n country full outcome
IND_BS3 0.8972731 0.013 282 IND 1 seroconversion
INDexp_BS3 0.8760109 0.214 149 IND (neo+) 0 seroconversion
INDunexp_BS3 2.1143769 0.008 132 IND (neo-) 0 seroconversion
MLW_BS3 3.2267416 0.085 56 MLW 1 seroconversionSummary plot
RV-IgA
Summary
R2 p n country full outcome
IND_BS3 0.3210798 0.501 282 IND 1 RV-IgA (post-ORV)
INDexp_BS3 0.7060590 0.376 149 IND (neo+) 0 RV-IgA (post-ORV)
INDunexp_BS3 1.3513704 0.082 132 IND (neo-) 0 RV-IgA (post-ORV)
MLW_BS3 3.8229274 0.039 56 MLW 1 RV-IgA (post-ORV)Summary plot
Dose 1 shedding
Summary
R2 p n country full outcome
IND_BS3 0.3485243 0.445 281 IND 1 dose 1 shedding
INDexp_BS3 0.6842036 0.399 147 IND (neo+) 0 dose 1 shedding
INDunexp_BS3 0.7761262 0.373 132 IND (neo-) 0 dose 1 shedding
MLW_BS3 1.6536110 0.561 47 MLW 1 dose 1 sheddingSummary plot
Random Forests/MaAsLin2
Column
Seroconversion
Summary plot
Differential features - FDR p <0.2
country n_tested_fisher n_signif_fisher n_tested_lr n_signif_lr
1 MLW 230 0 230 0
2 IND (neo-) 221 3 221 1
3 IND (neo+) 219 0 219 0
4 IND 219 11 219 14
n_tested_maaslin n_signif_maaslin
1 248 0
2 246 0
3 247 0
4 245 0
Summary of prevalence difference distribution
Proportion of features more prevalent in non-responders vs responders
country n_neg n_equal n_pos total proportion_neg
1 IND 179 2 38 219 81.7%
2 IND (neo+) 144 1 74 219 65.8%
3 IND (neo-) 173 11 37 221 78.3%
4 MLW 173 2 55 230 75.2%n = prevalence difference <0 (vs >=0).
P values (Wilcoxon test, mean of difference distribution = 0)
[,1]
IND 2.341528e-25
MLW 1.035777e-21
IND_exposed 9.568221e-09
IND_nonexposed 1.986182e-23Summary of adundance difference distribution
P values (Wilcoxon test, mean of difference distribution = 0)
[,1]
IND 3.259499e-02
MLW 6.841392e-07
IND_exposed 3.359604e-01
IND_nonexposed 7.889493e-08Proportion of features more abundant in non-responders vs responders
country n_neg n_equal n_pos total proportion_neg
1 IND 136 0 109 245 55.5%
2 IND (neo+) 131 0 116 247 53%
3 IND (neo-) 171 0 75 246 69.5%
4 MLW 156 0 92 248 62.9%Summary of MaAsLin2 associations
subset N_features FDR p<0.2 unadjusted FDR p<0.2 adjusted
1 IND 245 (109 +/136 -) 0 (0 +/0 -) 0 (0 +/0 -)
2 IND (neo+) 247 (116 +/131 -) 0 (0 +/0 -) 0 (0 +/0 -)
3 IND (neo-) 246 (75 +/171 -) 0 (0 +/0 -) 0 (0 +/0 -)
4 MLW 248 (92 +/156 -) 0 (0 +/0 -) 0 (0 +/0 -)Spearman’s rho matrix of statistical test p values - India
#### Rho values
Fisher p LR p LR (adj) p Wilcox p
Fisher p 1.00000000 0.99544780 0.93927813 0.79967926
LR p 0.99544780 1.00000000 0.94384184 0.80163413
LR (adj) p 0.93927813 0.94384184 1.00000000 0.78122636
Wilcox p 0.79967926 0.80163413 0.78122636 1.00000000
Maaslin p 0.21603651 0.22074299 0.20279228 0.33332572
Maaslin (adj) p 0.21608850 0.22424306 0.19002136 0.31598364
RF rank 0.12430392 0.12027731 0.06354611 0.04216527
Inv. abs. Maaslin coef. (adj) 0.10971458 0.11395697 0.05436722 0.14602237
Inv. abs. Prev. diff. 0.96880872 0.97128579 0.90461552 0.80803706
Inv. abs. ean abund. diff. 0.03092415 0.02905393 -0.01320164 0.04833137
Maaslin p Maaslin (adj) p RF rank
Fisher p 0.216036507 0.216088500 0.124303923
LR p 0.220742994 0.224243061 0.120277309
LR (adj) p 0.202792281 0.190021365 0.063546106
Wilcox p 0.333325717 0.315983639 0.042165275
Maaslin p 1.000000000 0.918332629 -0.001005404
Maaslin (adj) p 0.918332629 1.000000000 0.002227884
RF rank -0.001005404 0.002227884 1.000000000
Inv. abs. Maaslin coef. (adj) 0.508824706 0.574863756 0.261838061
Inv. abs. Prev. diff. 0.225818965 0.237883346 0.117876514
Inv. abs. ean abund. diff. 0.121547637 0.095248323 0.215807694
Inv. abs. Maaslin coef. (adj)
Fisher p 0.10971458
LR p 0.11395697
LR (adj) p 0.05436722
Wilcox p 0.14602237
Maaslin p 0.50882471
Maaslin (adj) p 0.57486376
RF rank 0.26183806
Inv. abs. Maaslin coef. (adj) 1.00000000
Inv. abs. Prev. diff. 0.16589524
Inv. abs. ean abund. diff. 0.75817291
Inv. abs. Prev. diff. Inv. abs. ean abund. diff.
Fisher p 0.96880872 0.03092415
LR p 0.97128579 0.02905393
LR (adj) p 0.90461552 -0.01320164
Wilcox p 0.80803706 0.04833137
Maaslin p 0.22581896 0.12154764
Maaslin (adj) p 0.23788335 0.09524832
RF rank 0.11787651 0.21580769
Inv. abs. Maaslin coef. (adj) 0.16589524 0.75817291
Inv. abs. Prev. diff. 1.00000000 0.08851936
Inv. abs. ean abund. diff. 0.08851936 1.00000000
N features with full data across tests: 219
Spearman’s rho matrix of statistical test p values - India (neo+)
#### Rho values
Fisher p LR p LR (adj) p Wilcox p
Fisher p 1.00000000 0.93962345 0.80945167 0.79348090
LR p 0.93962345 1.00000000 0.87375792 0.75986833
LR (adj) p 0.80945167 0.87375792 1.00000000 0.63148743
Wilcox p 0.79348090 0.75986833 0.63148743 1.00000000
Maaslin p 0.19139820 0.14728276 0.18134404 0.36526215
Maaslin (adj) p 0.18184050 0.12820348 0.15584905 0.34179853
RF rank 0.41528458 0.35976607 0.29400185 0.31327133
Inv. abs. Maaslin coef. (adj) 0.13295295 0.12386310 0.12308431 0.10811978
Inv. abs. prev. diff. 0.96351173 0.94747853 0.83400723 0.78526894
Inv. abs. mean abund. diff. 0.02814309 0.04879873 0.04904544 -0.06022941
Maaslin p Maaslin (adj) p RF rank
Fisher p 0.19139820 0.1818404955 0.41528458
LR p 0.14728276 0.1282034804 0.35976607
LR (adj) p 0.18134404 0.1558490523 0.29400185
Wilcox p 0.36526215 0.3417985307 0.31327133
Maaslin p 1.00000000 0.8025786329 0.09103020
Maaslin (adj) p 0.80257863 1.0000000000 0.09490557
RF rank 0.09103020 0.0949055720 1.00000000
Inv. abs. Maaslin coef. (adj) 0.34105705 0.4928776263 0.30183829
Inv. abs. prev. diff. 0.18295480 0.1744762162 0.40268269
Inv. abs. mean abund. diff. 0.09306614 -0.0009060061 0.23329487
Inv. abs. Maaslin coef. (adj)
Fisher p 0.1329529
LR p 0.1238631
LR (adj) p 0.1230843
Wilcox p 0.1081198
Maaslin p 0.3410570
Maaslin (adj) p 0.4928776
RF rank 0.3018383
Inv. abs. Maaslin coef. (adj) 1.0000000
Inv. abs. prev. diff. 0.1590364
Inv. abs. mean abund. diff. 0.7505695
Inv. abs. prev. diff. Inv. abs. mean abund. diff.
Fisher p 0.96351173 0.0281430865
LR p 0.94747853 0.0487987261
LR (adj) p 0.83400723 0.0490454374
Wilcox p 0.78526894 -0.0602294149
Maaslin p 0.18295480 0.0930661396
Maaslin (adj) p 0.17447622 -0.0009060061
RF rank 0.40268269 0.2332948690
Inv. abs. Maaslin coef. (adj) 0.15903641 0.7505695385
Inv. abs. prev. diff. 1.00000000 0.0734473430
Inv. abs. mean abund. diff. 0.07344734 1.0000000000
N features with full data across tests: 219
Spearman’s rho matrix of statistical test p values - India (neo-)
#### Rho values
Fisher p LR p LR (adj) p Wilcox p
Fisher p 1.00000000 0.96740470 0.90009933 0.77069001
LR p 0.96740470 1.00000000 0.93052145 0.74539875
LR (adj) p 0.90009933 0.93052145 1.00000000 0.63359756
Wilcox p 0.77069001 0.74539875 0.63359756 1.00000000
Maaslin p 0.36417401 0.36012485 0.29421882 0.52114690
Maaslin (adj) p 0.39906493 0.39681864 0.35999311 0.55702914
RF rank 0.15439014 0.18364292 0.23358533 -0.01969938
Inv. abs. Maaslin coef. (adj) 0.24381691 0.26013069 0.22675353 0.32834447
Inv. abs. prev. diff. 0.94481122 0.93774429 0.86309737 0.79822056
Inv. abs. mean abund. diff. 0.05435312 0.08138352 0.05697746 0.10239922
Maaslin p Maaslin (adj) p RF rank
Fisher p 0.3641740 0.39906493 0.15439014
LR p 0.3601249 0.39681864 0.18364292
LR (adj) p 0.2942188 0.35999311 0.23358533
Wilcox p 0.5211469 0.55702914 -0.01969938
Maaslin p 1.0000000 0.88909024 0.05472890
Maaslin (adj) p 0.8890902 1.00000000 0.04030262
RF rank 0.0547289 0.04030262 1.00000000
Inv. abs. Maaslin coef. (adj) 0.5704715 0.59530057 0.29330495
Inv. abs. prev. diff. 0.3713198 0.40224879 0.11652927
Inv. abs. mean abund. diff. 0.3094167 0.20663174 0.31107605
Inv. abs. Maaslin coef. (adj)
Fisher p 0.2438169
LR p 0.2601307
LR (adj) p 0.2267535
Wilcox p 0.3283445
Maaslin p 0.5704715
Maaslin (adj) p 0.5953006
RF rank 0.2933049
Inv. abs. Maaslin coef. (adj) 1.0000000
Inv. abs. prev. diff. 0.2873822
Inv. abs. mean abund. diff. 0.8025056
Inv. abs. prev. diff. Inv. abs. mean abund. diff.
Fisher p 0.9448112 0.05435312
LR p 0.9377443 0.08138352
LR (adj) p 0.8630974 0.05697746
Wilcox p 0.7982206 0.10239922
Maaslin p 0.3713198 0.30941674
Maaslin (adj) p 0.4022488 0.20663174
RF rank 0.1165293 0.31107605
Inv. abs. Maaslin coef. (adj) 0.2873822 0.80250559
Inv. abs. prev. diff. 1.0000000 0.10925293
Inv. abs. mean abund. diff. 0.1092529 1.00000000
N features with full data across tests: 221
Spearman’s rho matrix of statistical test p values - Malawi
#### Rho values
Fisher p LR p LR (adj) p Wilcox p
Fisher p 1.0000000 0.9115033 0.8428313 0.7632252
LR p 0.9115033 1.0000000 0.9110780 0.7380163
LR (adj) p 0.8428313 0.9110780 1.0000000 0.6742225
Wilcox p 0.7632252 0.7380163 0.6742225 1.0000000
Maaslin p 0.3497603 0.3112529 0.2579351 0.4921988
Maaslin (adj) p 0.3534166 0.3207310 0.2800458 0.4889001
RF rank 0.3627036 0.3246166 0.2932903 0.3533248
Inv. abs. maaslin coef. (adj) 0.2969255 0.2879519 0.2506379 0.3532784
Inv. abs. prev. diff. 0.9212737 0.9096664 0.7955558 0.7529547
Inv. abs. mean abund. diff. 0.1905314 0.1861532 0.1625839 0.1609818
Maaslin p Maaslin (adj) p RF rank
Fisher p 0.3497603 0.3534166 0.3627036
LR p 0.3112529 0.3207310 0.3246166
LR (adj) p 0.2579351 0.2800458 0.2932903
Wilcox p 0.4921988 0.4889001 0.3533248
Maaslin p 1.0000000 0.9021420 0.2553764
Maaslin (adj) p 0.9021420 1.0000000 0.1815415
RF rank 0.2553764 0.1815415 1.0000000
Inv. abs. maaslin coef. (adj) 0.5203509 0.5712180 0.4795953
Inv. abs. prev. diff. 0.3365121 0.3418944 0.2629649
Inv. abs. mean abund. diff. 0.2733555 0.2350667 0.4868071
Inv. abs. maaslin coef. (adj)
Fisher p 0.2969255
LR p 0.2879519
LR (adj) p 0.2506379
Wilcox p 0.3532784
Maaslin p 0.5203509
Maaslin (adj) p 0.5712180
RF rank 0.4795953
Inv. abs. maaslin coef. (adj) 1.0000000
Inv. abs. prev. diff. 0.2517086
Inv. abs. mean abund. diff. 0.8653168
Inv. abs. prev. diff. Inv. abs. mean abund. diff.
Fisher p 0.9212737 0.1905314
LR p 0.9096664 0.1861532
LR (adj) p 0.7955558 0.1625839
Wilcox p 0.7529547 0.1609818
Maaslin p 0.3365121 0.2733555
Maaslin (adj) p 0.3418944 0.2350667
RF rank 0.2629649 0.4868071
Inv. abs. maaslin coef. (adj) 0.2517086 0.8653168
Inv. abs. prev. diff. 1.0000000 0.1263993
Inv. abs. mean abund. diff. 0.1263993 1.0000000
N features with full data across tests: 230
RV-IgA
Summary plot
Differential features - p <0.2
country n_tested_wilcox n_signif_wilcox n_tested_lr n_signif_lr
1 MLW 220 0 220 0
2 IND (neo-) 216 0 216 0
3 IND (neo+) 216 0 216 0
4 IND 217 0 217 0
n_tested_maaslin n_signif_maaslin
1 246 0
2 244 0
3 245 0
4 245 0
Summary of GMRs
Proportion of features negatively vs positively correlated with RV-IgA
country n_neg n_equal n_pos total proportion_neg
1 IND 156 0 61 217 71.9%
2 IND (neo+) 104 0 112 216 48.1%
3 IND (neo-) 165 0 51 216 76.4%
4 MLW 157 0 63 220 71.4%n = GM ratio <1 (vs >=1).
P values (Wilcoxon test, mean of difference distribution = 1)
[,1]
IND 3.593035e-09
MLW 3.284286e-07
IND_exposed 3.785097e-02
IND_nonexposed 1.378226e-17Summary of adundance difference distribution
P values (Wilcoxon test, mean of difference distribution = 0)
[,1]
IND 5.317346e-02
MLW 2.956899e-07
IND_exposed 2.059736e-08
IND_nonexposed 2.485097e-04Proportion of features negatively vs positively correlated with RV-IgA
country n_neg n_equal n_pos total proportion_neg
1 IND 107 0 138 245 43.7%
2 IND (neo+) 78 0 167 245 31.8%
3 IND (neo-) 155 0 89 244 63.5%
4 MLW 155 0 91 246 63%Summary of MaAsLin2 associations
subset N_features FDR p<0.2 unadjusted FDR p<0.2 adjusted
1 IND 245 (138 +/107 -) 0 (0 +/0 -) 0 (0 +/0 -)
2 IND (neo+) 245 (167 +/78 -) 0 (0 +/0 -) 0 (0 +/0 -)
3 IND (neo-) 244 (89 +/155 -) 0 (0 +/0 -) 0 (0 +/0 -)
4 MLW 246 (91 +/155 -) 0 (0 +/0 -) 0 (0 +/0 -)Spearman’s rho matrix of statistical test p values - India
#### Rho values
Spearman p LR p LR (adj) p Wilcox p
Spearman p 1.00000000 0.06125838 -0.005594780 0.76410872
LR p 0.06125838 1.00000000 0.860873885 0.03564736
LR (adj) p -0.00559478 0.86087388 1.000000000 -0.06663239
Wilcox p 0.76410872 0.03564736 -0.066632394 1.00000000
Maaslin p 0.17420388 0.03677241 0.068760364 0.06330888
Maaslin (adj) p 0.22514645 0.08223763 0.127833209 0.10718047
RF rank 0.32936390 -0.03274778 -0.009694565 0.27373797
Inv. abs. maaslin coef. (adj) 0.11818444 -0.02481715 0.054489212 0.07607095
Inv. abs. GMR-1 0.70846193 0.07538391 0.003460919 0.92168744
Maaslin p Maaslin (adj) p RF rank
Spearman p 0.17420388 0.22514645 0.329363905
LR p 0.03677241 0.08223763 -0.032747784
LR (adj) p 0.06876036 0.12783321 -0.009694565
Wilcox p 0.06330888 0.10718047 0.273737967
Maaslin p 1.00000000 0.84654636 0.117632483
Maaslin (adj) p 0.84654636 1.00000000 0.124064601
RF rank 0.11763248 0.12406460 1.000000000
Inv. abs. maaslin coef. (adj) 0.51097112 0.61206002 0.131732174
Inv. abs. GMR-1 0.15111543 0.18295189 0.328828384
Inv. abs. maaslin coef. (adj) Inv. abs. GMR-1
Spearman p 0.11818444 0.708461929
LR p -0.02481715 0.075383907
LR (adj) p 0.05448921 0.003460919
Wilcox p 0.07607095 0.921687442
Maaslin p 0.51097112 0.151115433
Maaslin (adj) p 0.61206002 0.182951892
RF rank 0.13173217 0.328828384
Inv. abs. maaslin coef. (adj) 1.00000000 0.059734025
Inv. abs. GMR-1 0.05973402 1.000000000
N features with full data across tests: 217
Spearman’s rho matrix of statistical test p values - India (neo+)
#### Rho values
Spearman p LR p LR (adj) p Wilcox p
Spearman p 1.0000000 0.36643447 0.24110671 0.69062467
LR p 0.3664345 1.00000000 0.80811989 0.44837275
LR (adj) p 0.2411067 0.80811989 1.00000000 0.28991270
Wilcox p 0.6906247 0.44837275 0.28991270 1.00000000
Maaslin p 0.5444480 0.17075102 0.16050084 0.26843290
Maaslin (adj) p 0.3638076 0.08516772 0.10148490 0.16230267
RF rank 0.3381429 0.13413949 0.13311066 0.11554212
Inv. abs. maaslin coef. (adj) 0.2104681 0.01242096 0.02361066 0.05694287
Inv. abs. GMR-1 0.6241537 0.43643292 0.28836495 0.87850639
Maaslin p Maaslin (adj) p RF rank
Spearman p 0.5444480 0.36380762 0.3381429
LR p 0.1707510 0.08516772 0.1341395
LR (adj) p 0.1605008 0.10148490 0.1331107
Wilcox p 0.2684329 0.16230267 0.1155421
Maaslin p 1.0000000 0.76521392 0.3372343
Maaslin (adj) p 0.7652139 1.00000000 0.2389836
RF rank 0.3372343 0.23898356 1.0000000
Inv. abs. maaslin coef. (adj) 0.4976304 0.64686529 0.2611712
Inv. abs. GMR-1 0.2290513 0.14120316 0.1008538
Inv. abs. maaslin coef. (adj) Inv. abs. GMR-1
Spearman p 0.210468093 0.624153657
LR p 0.012420962 0.436432918
LR (adj) p 0.023610665 0.288364948
Wilcox p 0.056942875 0.878506387
Maaslin p 0.497630360 0.229051310
Maaslin (adj) p 0.646865288 0.141203158
RF rank 0.261171245 0.100853785
Inv. abs. maaslin coef. (adj) 1.000000000 0.006974363
Inv. abs. GMR-1 0.006974363 1.000000000
N features with full data across tests: 216
Spearman’s rho matrix of statistical test p values - India (neo-)
#### Rho values
Spearman p LR p LR (adj) p Wilcox p
Spearman p 1.0000000 0.4035604 0.25009109 0.7524476
LR p 0.4035604 1.0000000 0.86669048 0.5135462
LR (adj) p 0.2500911 0.8666905 1.00000000 0.3826076
Wilcox p 0.7524476 0.5135462 0.38260756 1.0000000
Maaslin p 0.4718275 0.1925862 0.07843151 0.3274521
Maaslin (adj) p 0.4743305 0.2203789 0.11258053 0.3002477
RF rank 0.3429429 0.1587373 0.07524381 0.2111230
Inv. abs. maaslin coef. (adj) 0.2290001 0.1306422 0.05011134 0.1113969
Inv. abs. GMR-1 0.6639219 0.5957823 0.45948154 0.9237833
Maaslin p Maaslin (adj) p RF rank
Spearman p 0.47182748 0.4743305 0.34294288
LR p 0.19258624 0.2203789 0.15873730
LR (adj) p 0.07843151 0.1125805 0.07524381
Wilcox p 0.32745210 0.3002477 0.21112302
Maaslin p 1.00000000 0.8565475 0.28281356
Maaslin (adj) p 0.85654747 1.0000000 0.26093190
RF rank 0.28281356 0.2609319 1.00000000
Inv. abs. maaslin coef. (adj) 0.55937080 0.6514676 0.06818371
Inv. abs. GMR-1 0.29992379 0.3018433 0.25633432
Inv. abs. maaslin coef. (adj) Inv. abs. GMR-1
Spearman p 0.22900011 0.66392193
LR p 0.13064218 0.59578228
LR (adj) p 0.05011134 0.45948154
Wilcox p 0.11139690 0.92378333
Maaslin p 0.55937080 0.29992379
Maaslin (adj) p 0.65146763 0.30184332
RF rank 0.06818371 0.25633432
Inv. abs. maaslin coef. (adj) 1.00000000 0.08310173
Inv. abs. GMR-1 0.08310173 1.00000000
N features with full data across tests: 216
Spearman’s rho matrix of statistical test p values - Malawi
#### Rho values
Spearman p LR p LR (adj) p Wilcox p
Spearman p 1.0000000 0.2102546 0.3123503 0.7529193
LR p 0.2102546 1.0000000 0.6980687 0.3102912
LR (adj) p 0.3123503 0.6980687 1.0000000 0.4668047
Wilcox p 0.7529193 0.3102912 0.4668047 1.0000000
Maaslin p 0.4758074 0.2265335 0.1845326 0.3223190
Maaslin (adj) p 0.4455836 0.2369965 0.2210901 0.3069986
RF rank 0.4074235 0.1724146 0.2383055 0.3855667
Inv. abs. maaslin coef. (adj) 0.3473265 0.2537758 0.2298891 0.2257241
Inv. abs. GMR-1 0.6270526 0.3808757 0.5330280 0.8271893
Maaslin p Maaslin (adj) p RF rank
Spearman p 0.4758074 0.4455836 0.4074235
LR p 0.2265335 0.2369965 0.1724146
LR (adj) p 0.1845326 0.2210901 0.2383055
Wilcox p 0.3223190 0.3069986 0.3855667
Maaslin p 1.0000000 0.9417850 0.2956425
Maaslin (adj) p 0.9417850 1.0000000 0.3202414
RF rank 0.2956425 0.3202414 1.0000000
Inv. abs. maaslin coef. (adj) 0.5072111 0.5660628 0.2001950
Inv. abs. GMR-1 0.2956882 0.2735980 0.3090177
Inv. abs. maaslin coef. (adj) Inv. abs. GMR-1
Spearman p 0.3473265 0.6270526
LR p 0.2537758 0.3808757
LR (adj) p 0.2298891 0.5330280
Wilcox p 0.2257241 0.8271893
Maaslin p 0.5072111 0.2956882
Maaslin (adj) p 0.5660628 0.2735980
RF rank 0.2001950 0.3090177
Inv. abs. maaslin coef. (adj) 1.0000000 0.1958437
Inv. abs. GMR-1 0.1958437 1.0000000
N features with full data across tests: 220
Dose 1 shedding
Summary plot
Differential features - FDR p <0.2
country n_tested_fisher n_signif_fisher n_tested_lr n_signif_lr
1 MLW 229 0 229 0
2 IND (neo-) 224 0 224 0
3 IND (neo+) 219 0 219 0
4 IND 223 0 223 0
n_tested_maaslin n_signif_maaslin
1 248 0
2 245 0
3 248 0
4 246 0
Summary of prevalence difference distribution
Proportion of features more prevalent in non-responders vs responders
country n_neg n_equal n_pos total proportion_neg
1 IND 157 1 65 223 70.4%
2 IND (neo+) 127 2 90 219 58%
3 IND (neo-) 160 1 63 224 71.4%
4 MLW 148 0 81 229 64.6%n = prevalence difference <0 (vs >=0).
P values (Wilcoxon test, mean of difference distribution = 0)
[,1]
IND 4.559072e-12
MLW 5.980349e-06
IND_exposed 3.613904e-05
IND_nonexposed 2.458974e-11Summary of adundance difference distribution
P values (Wilcoxon test, mean of difference distribution = 0)
[,1]
IND 0.59123080
MLW 0.24867428
IND_exposed 0.01234451
IND_nonexposed 0.16630766Proportion of features more abundant in non-responders vs responders
country n_neg n_equal n_pos total proportion_neg
1 IND 128 0 118 246 52%
2 IND (neo+) 159 0 89 248 64.1%
3 IND (neo-) 102 0 143 245 41.6%
4 MLW 116 0 132 248 46.8%Summary of MaAsLin2 associations
subset N_features FDR p<0.2 unadjusted FDR p<0.2 adjusted
1 IND 246 (118 +/128 -) 0 (0 +/0 -) 0 (0 +/0 -)
2 IND (neo+) 248 (89 +/159 -) 0 (0 +/0 -) 0 (0 +/0 -)
3 IND (neo-) 245 (143 +/102 -) 0 (0 +/0 -) 0 (0 +/0 -)
4 MLW 248 (132 +/116 -) 0 (0 +/0 -) 0 (0 +/0 -)Spearman’s rho matrix of statistical test p values - India
#### Rho values
Fisher p LR p LR (adj) p Wilcox p
Fisher p 1.00000000 0.99180445 0.923707317 0.68479534
LR p 0.99180445 1.00000000 0.939142371 0.69006102
LR (adj) p 0.92370732 0.93914237 1.000000000 0.63531044
Wilcox p 0.68479534 0.69006102 0.635310439 1.00000000
Maaslin p -0.01201308 -0.02351501 -0.018059499 0.17820675
Maaslin (adj) p -0.03695215 -0.04609183 -0.023605364 0.14453659
RF rank 0.34191358 0.32485086 0.314570095 0.16674602
Inv. abs. Maaslin coef. (adj) -0.01010707 -0.02722452 0.004627145 0.05862601
Inv. abs. prev. diff. 0.95125892 0.95547131 0.909375588 0.69156758
Inv. abs. mean abund. diff. -0.03346682 -0.04965850 -0.035705629 -0.03214978
Maaslin p Maaslin (adj) p RF rank
Fisher p -0.012013079 -0.03695215 0.34191358
LR p -0.023515013 -0.04609183 0.32485086
LR (adj) p -0.018059499 -0.02360536 0.31457010
Wilcox p 0.178206754 0.14453659 0.16674602
Maaslin p 1.000000000 0.95665785 0.04137053
Maaslin (adj) p 0.956657851 1.00000000 0.03756796
RF rank 0.041370527 0.03756796 1.00000000
Inv. abs. Maaslin coef. (adj) 0.594180143 0.63676481 0.27382720
Inv. abs. prev. diff. -0.003349486 -0.03428759 0.31968810
Inv. abs. mean abund. diff. 0.247084769 0.24877937 0.25188830
Inv. abs. Maaslin coef. (adj)
Fisher p -0.010107066
LR p -0.027224521
LR (adj) p 0.004627145
Wilcox p 0.058626011
Maaslin p 0.594180143
Maaslin (adj) p 0.636764808
RF rank 0.273827198
Inv. abs. Maaslin coef. (adj) 1.000000000
Inv. abs. prev. diff. 0.008328802
Inv. abs. mean abund. diff. 0.778038809
Inv. abs. prev. diff. Inv. abs. mean abund. diff.
Fisher p 0.951258923 -0.03346682
LR p 0.955471315 -0.04965850
LR (adj) p 0.909375588 -0.03570563
Wilcox p 0.691567579 -0.03214978
Maaslin p -0.003349486 0.24708477
Maaslin (adj) p -0.034287585 0.24877937
RF rank 0.319688104 0.25188830
Inv. abs. Maaslin coef. (adj) 0.008328802 0.77803881
Inv. abs. prev. diff. 1.000000000 -0.01341418
Inv. abs. mean abund. diff. -0.013414176 1.00000000
N features with full data across tests: 223
Spearman’s rho matrix of statistical test p values - India (neo+)
#### Rho values
Fisher p LR p LR (adj) p Wilcox p
Fisher p 1.00000000 0.861977026 0.70687569 0.73268375
LR p 0.86197703 1.000000000 0.85367036 0.68695347
LR (adj) p 0.70687569 0.853670359 1.00000000 0.54865813
Wilcox p 0.73268375 0.686953469 0.54865813 1.00000000
Maaslin p 0.29245235 0.264783161 0.21830635 0.48603631
Maaslin (adj) p 0.19092551 0.172671085 0.13787403 0.34658334
RF rank 0.24260242 0.246778334 0.24188422 0.20452089
Inv. abs. Maaslin coef. (adj) 0.11486324 0.085231306 0.02497972 0.12356987
Inv. abs. prev. diff. 0.95099619 0.893435753 0.73883799 0.74064383
Inv. abs. mean abund. diff. 0.03130903 0.009781606 -0.04355799 0.00863505
Maaslin p Maaslin (adj) p RF rank
Fisher p 0.2924524 0.1909255 0.2426024
LR p 0.2647832 0.1726711 0.2467783
LR (adj) p 0.2183064 0.1378740 0.2418842
Wilcox p 0.4860363 0.3465833 0.2045209
Maaslin p 1.0000000 0.8474813 0.2115233
Maaslin (adj) p 0.8474813 1.0000000 0.1139317
RF rank 0.2115233 0.1139317 1.0000000
Inv. abs. Maaslin coef. (adj) 0.4756132 0.5494556 0.3133250
Inv. abs. prev. diff. 0.2810726 0.1819297 0.2501355
Inv. abs. mean abund. diff. 0.2762736 0.2291110 0.2739589
Inv. abs. Maaslin coef. (adj)
Fisher p 0.11486324
LR p 0.08523131
LR (adj) p 0.02497972
Wilcox p 0.12356987
Maaslin p 0.47561324
Maaslin (adj) p 0.54945560
RF rank 0.31332503
Inv. abs. Maaslin coef. (adj) 1.00000000
Inv. abs. prev. diff. 0.10906792
Inv. abs. mean abund. diff. 0.87104322
Inv. abs. prev. diff. Inv. abs. mean abund. diff.
Fisher p 0.95099619 0.031309032
LR p 0.89343575 0.009781606
LR (adj) p 0.73883799 -0.043557988
Wilcox p 0.74064383 0.008635050
Maaslin p 0.28107263 0.276273607
Maaslin (adj) p 0.18192974 0.229111017
RF rank 0.25013554 0.273958893
Inv. abs. Maaslin coef. (adj) 0.10906792 0.871043221
Inv. abs. prev. diff. 1.00000000 0.024219860
Inv. abs. mean abund. diff. 0.02421986 1.000000000
N features with full data across tests: 219
Spearman’s rho matrix of statistical test p values - India (neo-)
#### Rho values
Fisher p LR p LR (adj) p Wilcox p
Fisher p 1.000000000 0.985214017 0.90360738 0.69621383
LR p 0.985214017 1.000000000 0.91939657 0.70436952
LR (adj) p 0.903607381 0.919396569 1.00000000 0.67281622
Wilcox p 0.696213826 0.704369521 0.67281622 1.00000000
Maaslin p -0.075864528 -0.067711176 -0.04050720 0.06584561
Maaslin (adj) p -0.055638377 -0.050400613 -0.01610187 0.05624173
RF rank 0.430685301 0.405955291 0.35320986 0.30183857
Inv. abs. Maaslin coef. (adj) -0.012474408 -0.012639391 0.01765216 0.07363442
Inv. abs. prev. diff. 0.949949247 0.960725264 0.88785919 0.69810301
Inv. abs. mean abund. diff. -0.008512358 -0.003893355 0.00528935 0.03077408
Maaslin p Maaslin (adj) p RF rank
Fisher p -0.07586453 -0.05563838 0.43068530
LR p -0.06771118 -0.05040061 0.40595529
LR (adj) p -0.04050720 -0.01610187 0.35320986
Wilcox p 0.06584561 0.05624173 0.30183857
Maaslin p 1.00000000 0.91860132 0.04623212
Maaslin (adj) p 0.91860132 1.00000000 0.03718984
RF rank 0.04623212 0.03718984 1.00000000
Inv. abs. Maaslin coef. (adj) 0.67218343 0.69243861 0.25086056
Inv. abs. prev. diff. -0.09656418 -0.05987578 0.37299861
Inv. abs. mean abund. diff. 0.34306855 0.28199124 0.27494128
Inv. abs. Maaslin coef. (adj)
Fisher p -0.012474408
LR p -0.012639391
LR (adj) p 0.017652165
Wilcox p 0.073634422
Maaslin p 0.672183429
Maaslin (adj) p 0.692438608
RF rank 0.250860559
Inv. abs. Maaslin coef. (adj) 1.000000000
Inv. abs. prev. diff. -0.003028225
Inv. abs. mean abund. diff. 0.794606022
Inv. abs. prev. diff. Inv. abs. mean abund. diff.
Fisher p 0.949949247 -0.008512358
LR p 0.960725264 -0.003893355
LR (adj) p 0.887859195 0.005289350
Wilcox p 0.698103011 0.030774076
Maaslin p -0.096564177 0.343068546
Maaslin (adj) p -0.059875780 0.281991245
RF rank 0.372998614 0.274941277
Inv. abs. Maaslin coef. (adj) -0.003028225 0.794606022
Inv. abs. prev. diff. 1.000000000 0.001188439
Inv. abs. mean abund. diff. 0.001188439 1.000000000
N features with full data across tests: 224
Spearman’s rho matrix of statistical test p values - Malawi
#### Rho values
Fisher p LR p LR (adj) p Wilcox p
Fisher p 1.0000000 0.681361374 5.124106e-01 0.5741419
LR p 0.6813614 1.000000000 8.346291e-01 0.5070473
LR (adj) p 0.5124106 0.834629138 1.000000e+00 0.4103660
Wilcox p 0.5741419 0.507047328 4.103660e-01 1.0000000
Maaslin p 0.1612689 0.124149471 7.318281e-02 0.4848453
Maaslin (adj) p 0.1452902 0.108343052 8.292423e-02 0.3989583
RF rank 0.1952502 0.003358646 -6.295425e-05 0.3143143
Inv. abs. Maaslin coef. (adj) 0.1469968 -0.007008087 -3.541226e-02 0.3250295
Inv. abs. prev. diff. 0.9436845 0.796859004 6.318681e-01 0.5993587
Inv. abs. mean abund. diff. 0.1412285 -0.064318413 -9.321176e-02 0.2662403
Maaslin p Maaslin (adj) p RF rank
Fisher p 0.16126893 0.14529024 1.952502e-01
LR p 0.12414947 0.10834305 3.358646e-03
LR (adj) p 0.07318281 0.08292423 -6.295425e-05
Wilcox p 0.48484528 0.39895826 3.143143e-01
Maaslin p 1.00000000 0.85135251 2.240804e-01
Maaslin (adj) p 0.85135251 1.00000000 1.964526e-01
RF rank 0.22408042 0.19645259 1.000000e+00
Inv. abs. Maaslin coef. (adj) 0.60046166 0.67102215 4.353442e-01
Inv. abs. prev. diff. 0.13849213 0.12717381 1.314276e-01
Inv. abs. mean abund. diff. 0.43303089 0.36479470 4.799426e-01
Inv. abs. Maaslin coef. (adj)
Fisher p 0.146996827
LR p -0.007008087
LR (adj) p -0.035412264
Wilcox p 0.325029541
Maaslin p 0.600461663
Maaslin (adj) p 0.671022154
RF rank 0.435344199
Inv. abs. Maaslin coef. (adj) 1.000000000
Inv. abs. prev. diff. 0.090154797
Inv. abs. mean abund. diff. 0.834577758
Inv. abs. prev. diff. Inv. abs. mean abund. diff.
Fisher p 0.94368449 0.14122846
LR p 0.79685900 -0.06431841
LR (adj) p 0.63186814 -0.09321176
Wilcox p 0.59935871 0.26624031
Maaslin p 0.13849213 0.43303089
Maaslin (adj) p 0.12717381 0.36479470
RF rank 0.13142761 0.47994264
Inv. abs. Maaslin coef. (adj) 0.09015480 0.83457776
Inv. abs. prev. diff. 1.00000000 0.06790691
Inv. abs. mean abund. diff. 0.06790691 1.00000000
N features with full data across tests: 229
Summary plots
Seroconversion
IgA
Dose 1 shedding
Session info
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur ... 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] Maaslin2_1.10.0 FSA_0.9.3 ALDEx2_1.28.1
[4] zCompositions_1.4.0-1 truncnorm_1.0-8 NADA_1.6-1.1
[7] survival_3.4-0 MASS_7.3-58.1 sjstats_0.18.1
[10] ggExtra_0.10.0 formattable_0.2.1 inlmisc_0.5.5
[13] wesanderson_0.3.6 phangorn_2.10.0 ape_5.6-2
[16] DECIPHER_2.24.0 RSQLite_2.2.18 Biostrings_2.64.1
[19] GenomeInfoDb_1.32.4 XVector_0.36.0 IRanges_2.30.1
[22] S4Vectors_0.34.0 BiocGenerics_0.42.0 cowplot_1.1.1
[25] scales_1.2.1 RVAideMemoire_0.9-81-2 DescTools_0.99.47
[28] ggsignif_0.6.4 binom_1.1-1.1 shiny_1.7.3
[31] randomcoloR_1.1.0.1 crossval_1.0.4 labdsv_2.0-1
[34] mgcv_1.8-41 nlme_3.1-160 ggpubr_0.4.0
[37] data.table_1.14.4 corrplot_0.92 vegan_2.6-4
[40] lattice_0.20-45 permute_0.9-7 randomForest_4.7-1.1
[43] matrixStats_0.62.0 lme4_1.1-30 Matrix_1.5-1
[46] reshape2_1.4.4 pheatmap_1.0.12 DT_0.26
[49] plotly_4.10.0 cluster_2.1.4 tidyr_1.2.1
[52] dplyr_1.0.10 magrittr_2.0.3 plyr_1.8.7
[55] kableExtra_1.3.4 gridExtra_2.3 RColorBrewer_1.1-3
[58] knitr_1.40 ggplot2_3.3.6 phyloseq_1.40.0
loaded via a namespace (and not attached):
[1] estimability_1.4.1 coda_0.19-4
[3] bit64_4.0.5 DelayedArray_0.22.0
[5] RCurl_1.98-1.9 generics_0.1.3
[7] terra_1.6-17 proxy_0.4-27
[9] bit_4.0.4 webshot_0.5.4
[11] xml2_1.3.3 httpuv_1.6.6
[13] SummarizedExperiment_1.26.1 assertthat_0.2.1
[15] xfun_0.34 jquerylib_0.1.4
[17] evaluate_0.17 promises_1.2.0.1
[19] DEoptimR_1.0-11 fansi_1.0.3
[21] readxl_1.4.1 igraph_1.3.5
[23] DBI_1.1.3 htmlwidgets_1.5.4
[25] purrr_0.3.5 ellipsis_0.3.2
[27] backports_1.4.1 V8_4.2.1
[29] insight_0.18.6 MatrixGenerics_1.8.1
[31] vctrs_0.5.0 Biobase_2.56.0
[33] sjlabelled_1.2.0 abind_1.4-5
[35] cachem_1.0.6 withr_2.5.0
[37] robustbase_0.95-0 rgdal_1.5-32
[39] emmeans_1.8.2 getopt_1.20.3
[41] svglite_2.1.0 lazyeval_0.2.2
[43] crayon_1.5.2 flexdashboard_0.6.0
[45] pkgconfig_2.0.3 labeling_0.4.2
[47] rlang_1.0.6 lifecycle_1.0.3
[49] miniUI_0.1.1.1 modelr_0.1.9
[51] cellranger_1.1.0 datawizard_0.6.3
[53] raster_3.6-3 carData_3.0-5
[55] lpsymphony_1.24.0 Rhdf5lib_1.18.2
[57] boot_1.3-28 viridisLite_0.4.1
[59] parameters_0.19.0 rootSolve_1.8.2.3
[61] bitops_1.0-7 rhdf5filters_1.8.0
[63] blob_1.2.3 stringr_1.4.1
[65] rstatix_0.7.0 memoise_2.0.1
[67] zlibbioc_1.42.0 compiler_4.2.1
[69] cli_3.4.1 ade4_1.7-19
[71] tidyselect_1.2.0 stringi_1.7.8
[73] highr_0.9 yaml_2.3.6
[75] grid_4.2.1 sass_0.4.2
[77] fastmatch_1.1-3 tools_4.2.1
[79] lmom_2.9 rstudioapi_0.14
[81] foreach_1.5.2 optparse_1.7.3
[83] gld_2.6.6 farver_2.1.1
[85] Rtsne_0.16 RcppZiggurat_0.1.6
[87] digest_0.6.30 quadprog_1.5-8
[89] Rcpp_1.0.9 GenomicRanges_1.48.0
[91] car_3.1-1 broom_1.0.1
[93] performance_0.10.0 later_1.3.0
[95] httr_1.4.4 effectsize_0.8.1
[97] colorspace_2.0-3 rvest_1.0.3
[99] splines_4.2.1 expm_0.999-6
[101] sp_1.5-0 multtest_2.52.0
[103] Exact_3.2 systemfonts_1.0.4
[105] xtable_1.8-4 jsonlite_1.8.3
[107] nloptr_2.0.3 Rfast_2.0.6
[109] R6_2.5.1 pillar_1.8.1
[111] htmltools_0.5.3 mime_0.12
[113] glue_1.6.2 fastmap_1.1.0
[115] minqa_1.2.5 BiocParallel_1.30.4
[117] class_7.3-20 codetools_0.2-18
[119] pcaPP_2.0-3 mvtnorm_1.1-3
[121] utf8_1.2.2 bslib_0.4.0
[123] tibble_3.1.8 curl_4.3.3
[125] biglm_0.9-2.1 rmarkdown_2.17
[127] biomformat_1.24.0 munsell_0.5.0
[129] e1071_1.7-12 rhdf5_2.40.0
[131] GenomeInfoDbData_1.2.8 iterators_1.0.14
[133] sjmisc_2.8.9 gtable_0.3.1
[135] bayestestR_0.13.0 .